Data Intake
| Index | stub | file | data_type | taxon_string | translation_table |
|---|---|---|---|---|---|
| 0 | KX808498-truncated | KX808498-truncated.gb | GenBank | Caulerpa_cliftonii_HV03798 | 11 |
| 1 | KY509313-truncated | KY509313-truncated.gb | GenBank | Avrainvillea_mazei_HV02664 | 11 |
| 2 | MH591083-truncated | MH591083-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 3 | MH591084-truncated | MH591084-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 4 | MH591085-truncated | MH591085-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 5 | NC_026795-truncated | NC_026795-truncated.txt | GenBank | Bryopsis_plumosa_WEST4718 | 11 |
| 6 | KY819064-truncated-cds | KY819064-truncated.cds.fasta | CDS | Chlorodesmis_fastigiata_HV03865 | 11 |
Orthofinder
| Orthogroup | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| OG0000000 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|28|psbE | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|6|psbE, Avrainvillea_mazei_HV02664|KY509313-truncated.gb|7|orf100 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|5|KY819064.1|psbE | — | — | Flabellia_petiolata_HV01202|MH591085-truncated.gb|0|psbE | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|5|psbE |
| OG0000001 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|22|rpl23 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|3|rpl23 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|1|KY819064.1|rpl23 | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|1|rpl23 | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|1|rpl23 |
| OG0000002 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|23|petA | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|0|petA | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|0|KY819064.1|petA | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|0|petA | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|0|petA |
| OG0000003 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|24|psaI | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|1|psaI | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|2|KY819064.1|psaI | Flabellia_petiolata_HV01202|MH591083-truncated.gb|1|psaI | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|2|psaI |
| OG0000004 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|26|petG | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|2|petG | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|3|KY819064.1|petG | Flabellia_petiolata_HV01202|MH591083-truncated.gb|0|petG | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|3|petG |
| OG0000005 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|27|rbcL | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|4|rbcL | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|4|KY819064.1|rbcL | Flabellia_petiolata_HV01202|MH591083-truncated.gb|2|rbcL | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|4|rbcL |
| OG0000006 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|29|rps18, Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|30|orf179 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|5|rps18 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|6|KY819064.1|rps18 | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|6|rps18 |
| Orthogroup | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| OG0000007 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|0|rps9 | — | — | — | — | — | — |
| OG0000008 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|1|rpoC1 | — | — | — | — | — | — |
| OG0000009 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|2|rpoC2 | — | — | — | — | — | — |
| OG0000010 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|3|psaB | — | — | — | — | — | — |
| OG0000011 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|4|psbZ | — | — | — | — | — | — |
| OG0000012 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|5|orf180 | — | — | — | — | — | — |
| OG0000013 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|6|orf116 | — | — | — | — | — | — |
| OG0000014 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|7|orf144 | — | — | — | — | — | — |
| OG0000015 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|8|orf519 | — | — | — | — | — | — |
| OG0000016 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|9|psbA | — | — | — | — | — | — |
| OG0000017 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|10|orf128 | — | — | — | — | — | — |
| OG0000018 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|11|rpoA | — | — | — | — | — | — |
| OG0000019 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|12|rps11 | — | — | — | — | — | — |
| OG0000020 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|13|rpl36 | — | — | — | — | — | — |
| OG0000021 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|14|infA | — | — | — | — | — | — |
| OG0000022 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|15|rps8 | — | — | — | — | — | — |
| OG0000023 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|16|rpl5 | — | — | — | — | — | — |
| OG0000024 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|17|rpl14 | — | — | — | — | — | — |
| OG0000025 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|18|rpl16 | — | — | — | — | — | — |
| OG0000026 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|19|rps3 | — | — | — | — | — | — |
| OG0000027 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|20|rps19 | — | — | — | — | — | — |
| OG0000028 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|21|rpl2 | — | — | — | — | — | — |
| OG0000029 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|25|ycf20 | — | — | — | — | — | — |
| Input | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| KX808498-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| KY509313-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| KY819064-truncated-cds.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| MH591083-truncated.protein | 3 | 3 | 3 | 3 | 0 | 0 | 3 |
| MH591084-truncated.protein | 2 | 2 | 2 | 0 | 2 | 0 | 2 |
| MH591085-truncated.protein | 1 | 1 | 1 | 0 | 0 | 1 | 1 |
| NC_026795-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
results/orthofinder/output/Orthogroup_Sequences/OG0000001.fa results/orthofinder/output/Orthogroup_Sequences/OG0000002.fa results/orthofinder/output/Orthogroup_Sequences/OG0000003.fa results/orthofinder/output/Orthogroup_Sequences/OG0000004.fa results/orthofinder/output/Orthogroup_Sequences/OG0000005.fa
results/orthofinder/orthosnap/OG0000000/OG0000000_orthosnap_0.fa
Alignment
results/alignment/trimmed_cds/OG0000005.trimmed.cds.alignment.fa results/alignment/trimmed_cds/OG0000002.trimmed.cds.alignment.fa
Supermatrix
General Characteristics ======================= 5 Number of taxa 2385 Alignment length 306 Parsimony informative sites 306 Variable sites 2055 Constant sites Character Frequencies ===================== T 3746 G 2296 C 1878 A 3864 - 141
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/supermatrix/supermatrix.cds.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 517623
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 5 sequences with 2385 nucleotide sites
Number of constant sites: 1470 (= 61.6352% of all sites)
Number of invariant (constant or ambiguous constant) sites: 1470 (= 61.6352% of all sites)
Number of parsimony informative sites: 306
Number of distinct site patterns: 333
ModelFinder
-----------
Best-fit model according to BIC: TIM2+F+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
TIM2+F+G4 -8644.524 17317.049 - 0.00536 17317.226 - 0.00553 17397.926 + 0.568
TIM2+F+I -8645.577 17319.154 - 0.00187 17319.332 - 0.00193 17400.032 + 0.198
GTR+F+G4 -8637.895 17307.790 + 0.549 17308.020 + 0.552 17400.222 + 0.18
TIM2+F+I+G4 -8643.755 17317.510 - 0.00426 17317.713 - 0.00434 17404.165 - 0.0251
GTR+F+I -8640.051 17312.102 + 0.0636 17312.332 + 0.0639 17404.534 - 0.0209
GTR+F+I+G4 -8637.276 17308.552 + 0.375 17308.810 + 0.372 17406.760 - 0.00686
TPM2u+F+I -8662.959 17351.917 - 1.44e-10 17352.071 - 1.5e-10 17427.018 - 2.74e-07
TPM2u+F+G4 -8663.083 17352.165 - 1.27e-10 17352.319 - 1.33e-10 17427.266 - 2.42e-07
TVM+F+G4 -8656.156 17342.312 - 1.75e-08 17342.515 - 1.79e-08 17428.966 - 1.03e-07
TVM+F+I -8657.334 17344.669 - 5.39e-09 17344.871 - 5.5e-09 17431.323 - 3.18e-08
TPM2u+F+I+G4 -8662.520 17353.040 - 8.2e-11 17353.218 - 8.46e-11 17433.918 - 8.69e-09
TVM+F+I+G4 -8655.724 17343.448 - 9.93e-09 17343.678 - 9.98e-09 17435.879 - 3.26e-09
TIM+F+G4 -8664.187 17356.373 - 1.55e-11 17356.551 - 1.6e-11 17437.251 - 1.64e-09
TIM+F+I -8665.228 17358.456 - 5.47e-12 17358.633 - 5.65e-12 17439.333 - 5.8e-10
TIM+F+I+G4 -8663.563 17357.127 - 1.06e-11 17357.329 - 1.08e-11 17443.781 - 6.27e-11
K3Pu+F+I -8682.883 17391.765 - 3.2e-19 17391.919 - 3.34e-19 17466.866 - 6.09e-16
K3Pu+F+G4 -8684.608 17395.216 - 5.7e-20 17395.370 - 5.95e-20 17470.316 - 1.08e-16
TN+F+G4 -8687.700 17401.400 - 2.59e-21 17401.554 - 2.7e-21 17476.501 - 4.93e-18
TN+F+I -8687.772 17401.544 - 2.41e-21 17401.698 - 2.51e-21 17476.645 - 4.58e-18
K3Pu+F+I+G4 -8684.009 17396.017 - 3.82e-20 17396.194 - 3.94e-20 17476.894 - 4.05e-18
TN+F+I+G4 -8686.938 17401.875 - 2.04e-21 17402.052 - 2.11e-21 17482.753 - 2.16e-19
TIM3+F+G4 -8687.180 17402.360 - 1.6e-21 17402.537 - 1.65e-21 17483.237 - 1.7e-19
TIM3+F+I -8687.222 17402.443 - 1.54e-21 17402.621 - 1.58e-21 17483.321 - 1.63e-19
TIM3+F+I+G4 -8686.492 17402.983 - 1.17e-21 17403.186 - 1.19e-21 17489.637 - 6.92e-21
HKY+F+I -8703.893 17431.786 - 6.52e-28 17431.918 - 6.89e-28 17501.110 - 2.23e-23
HKY+F+G4 -8706.824 17437.648 - 3.48e-29 17437.780 - 3.67e-29 17506.972 - 1.19e-24
TPM3u+F+I -8703.263 17432.526 - 4.51e-28 17432.680 - 4.71e-28 17507.627 - 8.58e-25
HKY+F+I+G4 -8706.070 17438.140 - 2.72e-29 17438.294 - 2.84e-29 17513.241 - 5.18e-26
TPM3u+F+G4 -8706.096 17438.192 - 2.65e-29 17438.346 - 2.77e-29 17513.293 - 5.05e-26
TPM3u+F+I+G4 -8705.389 17438.778 - 1.98e-29 17438.955 - 2.04e-29 17519.655 - 2.1e-27
F81+F+I -8719.214 17460.427 - 3.94e-34 17460.539 - 4.2e-34 17523.974 - 2.42e-28
F81+F+G4 -8722.344 17466.689 - 1.72e-35 17466.800 - 1.83e-35 17530.235 - 1.06e-29
F81+F+I+G4 -8721.576 17467.153 - 1.36e-35 17467.284 - 1.44e-35 17536.476 - 4.67e-31
SYM+G4 -8781.326 17588.651 - 5.65e-62 17588.805 - 5.9e-62 17663.752 - 1.07e-58
SYM+I -8781.958 17589.916 - 3e-62 17590.069 - 3.13e-62 17665.016 - 5.71e-59
TVMe+G4 -8788.184 17600.368 - 1.61e-64 17600.500 - 1.7e-64 17669.692 - 5.51e-60
SYM+I+G4 -8780.617 17589.235 - 4.22e-62 17589.412 - 4.35e-62 17670.112 - 4.47e-60
TVMe+I -8788.416 17600.832 - 1.28e-64 17600.964 - 1.35e-64 17670.156 - 4.37e-60
TVMe+I+G4 -8787.408 17600.816 - 1.29e-64 17600.970 - 1.35e-64 17675.916 - 2.45e-61
GTR+F -8790.985 17611.970 - 4.88e-67 17612.172 - 4.97e-67 17698.624 - 2.88e-66
TIM2e+I -8821.675 17665.350 - 1.25e-78 17665.461 - 1.33e-78 17728.896 - 7.68e-73
TIM2e+G4 -8822.942 17667.884 - 3.52e-79 17667.995 - 3.75e-79 17731.431 - 2.16e-73
TPM2+I -8827.241 17674.482 - 1.3e-80 17674.574 - 1.4e-80 17732.251 - 1.44e-73
TPM2+G4 -8828.311 17676.623 - 4.46e-81 17676.716 - 4.8e-81 17734.392 - 4.92e-74
TIM2e+I+G4 -8821.803 17667.606 - 4.04e-79 17667.738 - 4.27e-79 17736.930 - 1.38e-74
TPM2+I+G4 -8827.262 17676.523 - 4.68e-81 17676.634 - 5e-81 17740.070 - 2.88e-75
TIMe+I -8855.392 17732.785 - 2.84e-93 17732.896 - 3.03e-93 17796.331 - 1.75e-87
TIMe+G4 -8858.213 17738.427 - 1.69e-94 17738.538 - 1.8e-94 17801.973 - 1.04e-88
K3P+I -8862.515 17745.031 - 6.23e-96 17745.124 - 6.7e-96 17802.801 - 6.88e-89
TIMe+I+G4 -8857.149 17738.298 - 1.8e-94 17738.429 - 1.91e-94 17807.621 - 6.17e-90
K3P+G4 -8866.996 17753.992 - 7.05e-98 17754.085 - 7.59e-98 17811.762 - 7.79e-91
K3P+I+G4 -8865.784 17753.567 - 8.72e-98 17753.679 - 9.3e-98 17817.114 - 5.36e-92
TIM3e+I -8888.262 17798.523 - 1.51e-107 17798.635 - 1.61e-107 17862.070 - 9.27e-102
TIM3e+G4 -8888.442 17798.883 - 1.26e-107 17798.994 - 1.34e-107 17862.430 - 7.74e-102
TIM3e+I+G4 -8887.719 17799.439 - 9.55e-108 17799.570 - 1.01e-107 17868.762 - 3.27e-103
TPM3+I -8896.995 17813.990 - 6.61e-111 17814.083 - 7.11e-111 17871.759 - 7.3e-104
TPM3+G4 -8899.610 17819.219 - 4.84e-112 17819.312 - 5.21e-112 17876.989 - 5.34e-105
TPM3+I+G4 -8898.394 17818.788 - 6e-112 17818.900 - 6.4e-112 17882.335 - 3.69e-106
TNe+I -8913.640 17847.281 - 3.9e-118 17847.374 - 4.2e-118 17905.050 - 4.31e-111
JC+I -8924.092 17864.183 - 8.33e-122 17864.244 - 9.11e-122 17910.399 - 2.97e-112
TNe+G4 -8916.622 17853.244 - 1.98e-119 17853.337 - 2.13e-119 17911.014 - 2.18e-112
K2P+I -8921.214 17860.427 - 5.45e-121 17860.503 - 5.92e-121 17912.420 - 1.08e-112
TNe+I+G4 -8915.437 17852.875 - 2.38e-119 17852.986 - 2.54e-119 17916.421 - 1.46e-113
JC+G4 -8929.121 17874.242 - 5.45e-124 17874.302 - 5.96e-124 17920.457 - 1.94e-114
K2P+G4 -8925.819 17869.638 - 5.45e-123 17869.714 - 5.91e-123 17921.631 - 1.08e-114
JC+I+G4 -8927.689 17873.377 - 8.4e-124 17873.453 - 9.12e-124 17925.370 - 1.67e-115
K2P+I+G4 -8924.449 17868.897 - 7.89e-123 17868.990 - 8.49e-123 17926.667 - 8.71e-116
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: TIM2+F+G4
Rate parameter R:
A-C: 2.8978
A-G: 2.1991
A-T: 2.8978
C-G: 1.0000
C-T: 4.8497
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.3279
pi(C) = 0.1594
pi(G) = 0.1948
pi(T) = 0.3179
Rate matrix Q:
A -0.9711 0.2476 0.2297 0.4938
C 0.5094 -1.44 0.1045 0.8265
G 0.3866 0.08544 -0.6424 0.1704
T 0.5094 0.4143 0.1045 -1.028
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.4419
Category Relative_rate Proportion
1 0.02319 0.25
2 0.2123 0.25
3 0.7729 0.25
4 2.992 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -8644.5237 (s.e. 119.3831)
Unconstrained log-likelihood (without tree): -8461.5941
Number of free parameters (#branches + #model parameters): 14
Akaike information criterion (AIC) score: 17317.0475
Corrected Akaike information criterion (AICc) score: 17317.2247
Bayesian information criterion (BIC) score: 17397.9248
Total tree length (sum of branch lengths): 0.8645
Sum of internal branch lengths: 0.1208 (13.9718% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Avrainvillea_mazei_HV02664' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+--------------------------------------------------Avrainvillea_mazei_HV02664
|
+------------------------------------------------Bryopsis_plumosa_WEST4718
|
| +----------------------------------------Caulerpa_cliftonii_HV03798
+-----------------| (100)
| +-----------------------Chlorodesmis_fastigiata_HV03865
+----------| (98)
+------------------Flabellia_petiolata_HV01202
Tree in newick format:
(Avrainvillea_mazei_HV02664:0.2056759698,Bryopsis_plumosa_WEST4718:0.1993162042,(Caulerpa_cliftonii_HV03798:0.1651556415,(Chlorodesmis_fastigiata_HV03865:0.0968946026,Flabellia_petiolata_HV01202:0.0766741283)98:0.0449103364)100:0.0758765985);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -8644.523737
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+--------------------------------------------------Avrainvillea_mazei_HV02664
|
+------------------------------------------------Bryopsis_plumosa_WEST4718
|
| +----------------------------------------Caulerpa_cliftonii_HV03798
+-----------------| (100)
| +-----------------------Chlorodesmis_fastigiata_HV03865
+----------| (98)
+------------------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Avrainvillea_mazei_HV02664:0.2056779360,Bryopsis_plumosa_WEST4718:0.1993172082,(Caulerpa_cliftonii_HV03798:0.1651639859,(Chlorodesmis_fastigiata_HV03865:0.0968984226,Flabellia_petiolata_HV01202:0.0766746704)98:0.0448985134)100:0.0758763348);
TIME STAMP
----------
Date and time: Mon Oct 2 04:12:08 2023
Total CPU time used: 0.815398 seconds (0h:0m:0s)
Total wall-clock time used: 0.8454933837 seconds (0h:0m:0s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/supermatrix/supermatrix.cds.fa -bb 1000 -m TEST -nt 1 -redo
Seed: 517623 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:12:07 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/supermatrix/supermatrix.cds.fa ... Fasta format detected
Reading fasta file: done in 0.0002525 secs
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00213237 secs
Alignment has 5 sequences with 2385 columns, 333 distinct patterns
306 parsimony-informative, 609 singleton sites, 1470 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.00955e-05 secs
1 Avrainvillea_mazei_HV02664 1.01% passed 32.15%
2 Bryopsis_plumosa_WEST4718 0.38% passed 79.51%
3 Caulerpa_cliftonii_HV03798 0.88% passed 49.91%
4 Chlorodesmis_fastigiata_HV03865 1.38% passed 92.09%
5 Flabellia_petiolata_HV01202 2.26% passed 94.37%
**** TOTAL 1.18% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 2.06307e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.000987813 secs using 99.82% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -8637.254
Optimal log-likelihood: -8637.251
Rate parameters: A-C: 2.96313 A-G: 2.93933 A-T: 4.21828 C-G: 2.01322 C-T: 6.41081 G-T: 1.00000
Base frequencies: A: 0.328 C: 0.159 G: 0.195 T: 0.318
Proportion of invariable sites: 0.308
Gamma shape alpha: 1.115
Parameters optimization took 1 rounds (0.002 sec)
Time for fast ML tree search: 0.012 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 88 DNA models (sample size: 2385) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 8790.985 15 17611.970 17612.172 17698.624
2 GTR+F+I 8640.051 16 17312.102 17312.332 17404.534
3 GTR+F+G4 8637.895 16 17307.790 17308.020 17400.222
4 GTR+F+I+G4 8637.276 17 17308.552 17308.810 17406.760
6 SYM+I 8781.958 13 17589.916 17590.069 17665.016
7 SYM+G4 8781.326 13 17588.651 17588.805 17663.752
8 SYM+I+G4 8780.617 14 17589.235 17589.412 17670.112
10 TVM+F+I 8657.334 15 17344.669 17344.871 17431.323
11 TVM+F+G4 8656.156 15 17342.312 17342.515 17428.966
12 TVM+F+I+G4 8655.724 16 17343.448 17343.678 17435.879
14 TVMe+I 8788.416 12 17600.832 17600.964 17670.156
15 TVMe+G4 8788.184 12 17600.368 17600.500 17669.692
16 TVMe+I+G4 8787.408 13 17600.816 17600.970 17675.916
18 TIM3+F+I 8687.222 14 17402.443 17402.621 17483.321
19 TIM3+F+G4 8687.180 14 17402.360 17402.537 17483.237
20 TIM3+F+I+G4 8686.492 15 17402.983 17403.186 17489.637
22 TIM3e+I 8888.262 11 17798.523 17798.635 17862.070
23 TIM3e+G4 8888.442 11 17798.883 17798.994 17862.430
24 TIM3e+I+G4 8887.719 12 17799.439 17799.570 17868.762
26 TIM2+F+I 8645.577 14 17319.154 17319.332 17400.032
27 TIM2+F+G4 8644.524 14 17317.049 17317.226 17397.926
28 TIM2+F+I+G4 8643.755 15 17317.510 17317.713 17404.165
30 TIM2e+I 8821.675 11 17665.350 17665.461 17728.896
31 TIM2e+G4 8822.942 11 17667.884 17667.995 17731.431
32 TIM2e+I+G4 8821.803 12 17667.606 17667.738 17736.930
34 TIM+F+I 8665.228 14 17358.456 17358.633 17439.333
35 TIM+F+G4 8664.187 14 17356.373 17356.551 17437.251
36 TIM+F+I+G4 8663.563 15 17357.127 17357.329 17443.781
38 TIMe+I 8855.392 11 17732.785 17732.896 17796.331
39 TIMe+G4 8858.213 11 17738.427 17738.538 17801.973
40 TIMe+I+G4 8857.149 12 17738.298 17738.429 17807.621
42 TPM3u+F+I 8703.263 13 17432.526 17432.680 17507.627
43 TPM3u+F+G4 8706.096 13 17438.192 17438.346 17513.293
44 TPM3u+F+I+G4 8705.389 14 17438.778 17438.955 17519.655
46 TPM3+I 8896.995 10 17813.990 17814.083 17871.759
47 TPM3+G4 8899.610 10 17819.219 17819.312 17876.989
48 TPM3+I+G4 8898.394 11 17818.788 17818.900 17882.335
50 TPM2u+F+I 8662.959 13 17351.917 17352.071 17427.018
51 TPM2u+F+G4 8663.083 13 17352.165 17352.319 17427.266
52 TPM2u+F+I+G4 8662.520 14 17353.040 17353.218 17433.918
54 TPM2+I 8827.241 10 17674.482 17674.574 17732.251
55 TPM2+G4 8828.311 10 17676.623 17676.716 17734.392
56 TPM2+I+G4 8827.262 11 17676.523 17676.634 17740.070
58 K3Pu+F+I 8682.883 13 17391.765 17391.919 17466.866
59 K3Pu+F+G4 8684.608 13 17395.216 17395.370 17470.316
60 K3Pu+F+I+G4 8684.009 14 17396.017 17396.194 17476.894
62 K3P+I 8862.515 10 17745.031 17745.124 17802.801
63 K3P+G4 8866.996 10 17753.992 17754.085 17811.762
64 K3P+I+G4 8865.784 11 17753.567 17753.679 17817.114
66 TN+F+I 8687.772 13 17401.544 17401.698 17476.645
67 TN+F+G4 8687.700 13 17401.400 17401.554 17476.501
68 TN+F+I+G4 8686.938 14 17401.875 17402.052 17482.753
70 TNe+I 8913.640 10 17847.281 17847.374 17905.050
71 TNe+G4 8916.622 10 17853.244 17853.337 17911.014
72 TNe+I+G4 8915.437 11 17852.875 17852.986 17916.421
74 HKY+F+I 8703.893 12 17431.786 17431.918 17501.110
75 HKY+F+G4 8706.824 12 17437.648 17437.780 17506.972
76 HKY+F+I+G4 8706.070 13 17438.140 17438.294 17513.241
78 K2P+I 8921.214 9 17860.427 17860.503 17912.420
79 K2P+G4 8925.819 9 17869.638 17869.714 17921.631
80 K2P+I+G4 8924.449 10 17868.897 17868.990 17926.667
82 F81+F+I 8719.214 11 17460.427 17460.539 17523.974
83 F81+F+G4 8722.344 11 17466.689 17466.800 17530.235
84 F81+F+I+G4 8721.576 12 17467.153 17467.284 17536.476
86 JC+I 8924.092 8 17864.183 17864.244 17910.399
87 JC+G4 8929.121 8 17874.242 17874.302 17920.457
88 JC+I+G4 8927.689 9 17873.377 17873.453 17925.370
Akaike Information Criterion: GTR+F+G4
Corrected Akaike Information Criterion: GTR+F+G4
Bayesian Information Criterion: TIM2+F+G4
Best-fit model: TIM2+F+G4 chosen according to BIC
All model information printed to results/supermatrix/supermatrix.cds.fa.model.gz
CPU time for ModelFinder: 0.381 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.386 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 517623)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -8644.524
Optimal log-likelihood: -8644.524
Rate parameters: A-C: 2.89399 A-G: 2.20137 A-T: 2.89399 C-G: 1.00000 C-T: 4.84920 G-T: 1.00000
Base frequencies: A: 0.328 C: 0.159 G: 0.195 T: 0.318
Gamma shape alpha: 0.442
Parameters optimization took 1 rounds (0.001 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000253439 secs using 96.28% CPU
Computing ML distances took 0.000296 sec (of wall-clock time) 0.000288 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.00394e-05 secs using 94.91% CPU
Constructing RapidNJ tree: done in 3.1732e-05 secs using 94.54% CPU
Computing RapidNJ tree took 0.000134 sec (of wall-clock time) 0.000129 sec (of CPU time)
Log-likelihood of RapidNJ tree: -8644.524
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.029 second
Computing log-likelihood of 4 initial trees ... 0.002 seconds
Current best score: -8644.524
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.00135605 secs using 99.85% CPU
Optimizing NNI: done in 0.00286522 secs using 99.54% CPU
Optimizing NNI: done in 0.00282393 secs
Optimizing NNI: done in 0.00281788 secs using 72.36% CPU
Optimizing NNI: done in 0.00276113 secs using 97.71% CPU
Finish initializing candidate tree set (5)
Current best tree score: -8644.524 / CPU time: 0.048
Number of iterations: 5
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00395259 secs using 99.96% CPU
Optimizing NNI: done in 0.00393617 secs using 99.94% CPU
Optimizing NNI: done in 0.00121167 secs using 99.86% CPU
Optimizing NNI: done in 0.00277851 secs using 99.91% CPU
Optimizing NNI: done in 0.00401989 secs using 99.95% CPU
Iteration 10 / LogL: -8644.813 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00280948 secs using 99.95% CPU
Optimizing NNI: done in 0.00242212 secs using 99.38% CPU
UPDATE BEST LOG-LIKELIHOOD: -8644.524
Optimizing NNI: done in 0.00249852 secs using 95.58% CPU
UPDATE BEST LOG-LIKELIHOOD: -8644.524
Optimizing NNI: done in 0.00269824 secs using 99.92% CPU
Optimizing NNI: done in 0.00120905 secs using 99.5% CPU
Optimizing NNI: done in 0.00116768 secs using 99.86% CPU
Optimizing NNI: done in 0.0039612 secs using 99.74% CPU
Optimizing NNI: done in 0.0038994 secs using 99.89% CPU
Optimizing NNI: done in 0.00412722 secs using 99.95% CPU
Optimizing NNI: done in 0.00123261 secs using 99.79% CPU
Iteration 20 / LogL: -8653.126 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00243481 secs using 99.88% CPU
Optimizing NNI: done in 0.0026633 secs using 99.95% CPU
Optimizing NNI: done in 0.00389514 secs using 99.95% CPU
Optimizing NNI: done in 0.00402337 secs using 99.94% CPU
Optimizing NNI: done in 0.00109873 secs using 99.84% CPU
Optimizing NNI: done in 0.00265146 secs using 99.91% CPU
Optimizing NNI: done in 0.00259072 secs using 99.93% CPU
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Optimizing NNI: done in 0.00121771 secs using 99.78% CPU
Optimizing NNI: done in 0.00400976 secs using 99.93% CPU
Iteration 30 / LogL: -8644.813 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00389909 secs using 99.95% CPU
Optimizing NNI: done in 0.00244047 secs using 99.94% CPU
Optimizing NNI: done in 0.00242224 secs using 99.91% CPU
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Optimizing NNI: done in 0.00120568 secs using 99.86% CPU
Optimizing NNI: done in 0.00414733 secs using 99.94% CPU
Iteration 40 / LogL: -8644.813 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00248268 secs using 99.93% CPU
Optimizing NNI: done in 0.00257837 secs using 99.95% CPU
Optimizing NNI: done in 0.00271951 secs using 99.91% CPU
Optimizing NNI: done in 0.00258329 secs using 99.91% CPU
Optimizing NNI: done in 0.00256454 secs using 99.9% CPU
Optimizing NNI: done in 0.00400297 secs using 97.55% CPU
Optimizing NNI: done in 0.00254933 secs using 99.87% CPU
Optimizing NNI: done in 0.00114062 secs using 99.77% CPU
Optimizing NNI: done in 0.00234947 secs using 99.9% CPU
Optimizing NNI: done in 0.00400686 secs using 99.95% CPU
Iteration 50 / LogL: -8644.758 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -8669.696
Optimizing NNI: done in 0.00241208 secs using 97.92% CPU
Optimizing NNI: done in 0.00261144 secs using 99.94% CPU
Optimizing NNI: done in 0.00402357 secs using 99.94% CPU
Optimizing NNI: done in 0.00401137 secs using 99.94% CPU
Optimizing NNI: done in 0.00387222 secs using 99.94% CPU
Optimizing NNI: done in 0.00115717 secs using 99.81% CPU
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Optimizing NNI: done in 0.00258704 secs using 99.92% CPU
Optimizing NNI: done in 0.00127187 secs using 99.77% CPU
Iteration 60 / LogL: -8656.526 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00400563 secs using 99.96% CPU
Optimizing NNI: done in 0.00110263 secs using 99.76% CPU
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Optimizing NNI: done in 0.00407155 secs using 99.94% CPU
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Optimizing NNI: done in 0.00429823 secs using 99.95% CPU
Optimizing NNI: done in 0.00429542 secs using 99.94% CPU
Iteration 70 / LogL: -8644.781 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00268806 secs using 99.92% CPU
Optimizing NNI: done in 0.00130914 secs using 99.84% CPU
Optimizing NNI: done in 0.00433993 secs using 99.96% CPU
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Optimizing NNI: done in 0.00286625 secs using 99.92% CPU
Iteration 80 / LogL: -8644.668 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00293162 secs using 99.91% CPU
Optimizing NNI: done in 0.00435475 secs using 99.96% CPU
Optimizing NNI: done in 0.00286919 secs using 99.92% CPU
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Optimizing NNI: done in 0.00424006 secs using 97.31% CPU
Optimizing NNI: done in 0.00255472 secs using 99.35% CPU
Iteration 90 / LogL: -8644.524 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00436692 secs using 99.91% CPU
Optimizing NNI: done in 0.00293647 secs using 99.92% CPU
Optimizing NNI: done in 0.00292062 secs using 99.94% CPU
Optimizing NNI: done in 0.00122836 secs using 99.81% CPU
Optimizing NNI: done in 0.00276098 secs using 99.93% CPU
Optimizing NNI: done in 0.00269005 secs using 99.92% CPU
Optimizing NNI: done in 0.00120115 secs using 99.82% CPU
Optimizing NNI: done in 0.00258955 secs using 99.9% CPU
Optimizing NNI: done in 0.00118079 secs using 99.85% CPU
Optimizing NNI: done in 0.00248631 secs using 99.91% CPU
Iteration 100 / LogL: -8644.524 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -8669.696
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00255194 secs using 99.88% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -8644.524
Optimal log-likelihood: -8644.524
Rate parameters: A-C: 2.89783 A-G: 2.19908 A-T: 2.89783 C-G: 1.00000 C-T: 4.84972 G-T: 1.00000
Base frequencies: A: 0.328 C: 0.159 G: 0.195 T: 0.318
Gamma shape alpha: 0.442
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -8644.524
Creating bootstrap support values...
Split supports printed to NEXUS file results/supermatrix/supermatrix.cds.fa.splits.nex
Total tree length: 0.865
Total number of iterations: 101
CPU time used for tree search: 0.742 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.760 sec (0h:0m:0s)
Total CPU time used: 0.815 sec (0h:0m:0s)
Total wall-clock time used: 0.838 sec (0h:0m:0s)
Computing bootstrap consensus tree...
Reading input file results/supermatrix/supermatrix.cds.fa.splits.nex...
5 taxa and 10 splits.
Consensus tree written to results/supermatrix/supermatrix.cds.fa.contree
Reading input trees file results/supermatrix/supermatrix.cds.fa.contree
Log-likelihood of consensus tree: -8644.524
Analysis results written to:
IQ-TREE report: results/supermatrix/supermatrix.cds.fa.iqtree
Maximum-likelihood tree: results/supermatrix/supermatrix.cds.fa.treefile
Likelihood distances: results/supermatrix/supermatrix.cds.fa.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/supermatrix/supermatrix.cds.fa.splits.nex
Consensus tree: results/supermatrix/supermatrix.cds.fa.contree
Screen log file: results/supermatrix/supermatrix.cds.fa.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/supermatrix/supermatrix.cds.fa.treefile -m "TIM2{2.89783,2.19908,4.84972}+F{0.327902,0.159369,0.19484,0.317889}+G4{0.441906}" --length 2385
Date and Time: Mon Oct 2 04:12:08 2023
Gene Tree
OG0000005
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/alignment/trimmed_cds/OG0000005.trimmed.cds.alignment.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 29709
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 5 sequences with 1425 nucleotide sites
Number of constant sites: 980 (= 68.7719% of all sites)
Number of invariant (constant or ambiguous constant) sites: 980 (= 68.7719% of all sites)
Number of parsimony informative sites: 165
Number of distinct site patterns: 191
ModelFinder
-----------
Best-fit model according to BIC: GTR+F+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
GTR+F+G4 -4700.958 9433.916 + 0.493 9434.303 + 0.495 9518.107 + 0.615
GTR+F+I -4701.476 9434.951 + 0.294 9435.338 + 0.295 9519.142 + 0.366
GTR+F+I+G4 -4700.796 9435.591 + 0.213 9436.026 + 0.209 9525.044 - 0.0192
SYM+I -4755.755 9537.510 - 1.58e-23 9537.768 - 1.69e-23 9605.915 - 5.26e-20
SYM+G4 -4756.304 9538.609 - 9.1e-24 9538.867 - 9.75e-24 9607.014 - 3.04e-20
SYM+I+G4 -4756.016 9540.031 - 4.47e-24 9540.329 - 4.7e-24 9613.698 - 1.07e-21
HKY+F+I -4768.665 9561.330 - 1.06e-28 9561.551 - 1.16e-28 9624.474 - 4.91e-24
HKY+F+G4 -4770.979 9565.958 - 1.05e-29 9566.179 - 1.14e-29 9629.101 - 4.86e-25
HKY+F+I+G4 -4771.601 9569.201 - 2.07e-30 9569.459 - 2.22e-30 9637.607 - 6.91e-27
F81+F+I -4780.098 9582.196 - 3.12e-33 9582.383 - 3.47e-33 9640.077 - 2.01e-27
F81+F+G4 -4782.764 9587.527 - 2.17e-34 9587.714 - 2.41e-34 9645.408 - 1.4e-28
F81+F+I+G4 -4783.308 9590.615 - 4.63e-35 9590.836 - 5.06e-35 9653.758 - 2.15e-30
GTR+F -4788.371 9606.743 - 1.46e-38 9607.083 - 1.5e-38 9685.671 - 2.53e-37
K2P+I -4853.060 9724.119 - 4.74e-64 9724.247 - 5.43e-64 9771.477 - 5.89e-56
JC+I -4857.312 9730.625 - 1.83e-65 9730.726 - 2.13e-65 9772.720 - 3.16e-56
K2P+G4 -4856.331 9730.661 - 1.8e-65 9730.789 - 2.06e-65 9778.019 - 2.24e-57
JC+G4 -4860.963 9737.926 - 4.76e-67 9738.028 - 5.52e-67 9780.021 - 8.22e-58
K2P+I+G4 -4856.646 9733.292 - 4.83e-66 9733.448 - 5.45e-66 9785.912 - 4.32e-59
JC+I+G4 -4861.282 9740.565 - 1.27e-67 9740.692 - 1.46e-67 9787.922 - 1.58e-59
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: GTR+F+G4
Rate parameter R:
A-C: 2.0503
A-G: 2.0515
A-T: 4.5040
C-G: 0.9119
C-T: 6.9541
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.2984
pi(C) = 0.1627
pi(G) = 0.2248
pi(T) = 0.3141
Rate matrix Q:
A -0.9876 0.1491 0.2062 0.6324
C 0.2735 -1.342 0.09165 0.9764
G 0.2736 0.06631 -0.4803 0.1404
T 0.6007 0.5056 0.1005 -1.207
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.3559
Category Relative_rate Proportion
1 0.0109 0.25
2 0.1481 0.25
3 0.6787 0.25
4 3.162 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -4700.9560 (s.e. 92.9611)
Unconstrained log-likelihood (without tree): -4367.3454
Number of free parameters (#branches + #model parameters): 16
Akaike information criterion (AIC) score: 9433.9121
Corrected Akaike information criterion (AICc) score: 9434.2984
Bayesian information criterion (BIC) score: 9518.1029
Total tree length (sum of branch lengths): 0.6525
Sum of internal branch lengths: 0.0950 (14.5631% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Caulerpa_cliftonii_HV03798' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+---------------------------------Caulerpa_cliftonii_HV03798
|
| +------------------------------------------Avrainvillea_mazei_HV02664
+-------------| (94)
| +--------------------------------------------Bryopsis_plumosa_WEST4718
|
| +-----------------Chlorodesmis_fastigiata_HV03865
+-----------| (97)
+-------------------Flabellia_petiolata_HV01202
Tree in newick format:
(Caulerpa_cliftonii_HV03798:0.1182267020,(Avrainvillea_mazei_HV02664:0.1499108882,Bryopsis_plumosa_WEST4718:0.1558503834)94:0.0519142452,(Chlorodesmis_fastigiata_HV03865:0.0624695653,Flabellia_petiolata_HV01202:0.0709881079)97:0.0431046277);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -4700.956027
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+---------------------------------Caulerpa_cliftonii_HV03798
|
| +------------------------------------------Avrainvillea_mazei_HV02664
+-------------| (94)
| +--------------------------------------------Bryopsis_plumosa_WEST4718
|
| +-----------------Chlorodesmis_fastigiata_HV03865
+-----------| (97)
+-------------------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Caulerpa_cliftonii_HV03798:0.1182189528,(Avrainvillea_mazei_HV02664:0.1499087060,Bryopsis_plumosa_WEST4718:0.1558512537)94:0.0519137718,(Chlorodesmis_fastigiata_HV03865:0.0624651131,Flabellia_petiolata_HV01202:0.0709877630)97:0.0431029002);
TIME STAMP
----------
Date and time: Mon Oct 2 04:11:46 2023
Total CPU time used: 0.732793 seconds (0h:0m:0s)
Total wall-clock time used: 0.7460586429 seconds (0h:0m:0s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000005.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000005/OG0000005.cds -redo
Seed: 29709 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:11:46 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000005.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.000181206 secs
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00129041 secs
Alignment has 5 sequences with 1425 columns, 191 distinct patterns
165 parsimony-informative, 280 singleton sites, 980 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 8.3074e-06 secs
1 Caulerpa_cliftonii_HV03798 0.00% passed 45.83%
2 Avrainvillea_mazei_HV02664 0.00% passed 78.45%
3 Chlorodesmis_fastigiata_HV03865 0.00% passed 84.29%
4 Flabellia_petiolata_HV01202 0.00% passed 92.04%
5 Bryopsis_plumosa_WEST4718 0.00% passed 90.76%
**** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 2.00793e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.000684097 secs using 66.36% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -4700.813
Optimal log-likelihood: -4700.803
Rate parameters: A-C: 2.05463 A-G: 2.04042 A-T: 4.51400 C-G: 0.90687 C-T: 6.96803 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.163 G: 0.225 T: 0.314
Proportion of invariable sites: 0.343
Gamma shape alpha: 0.943
Parameters optimization took 1 rounds (0.002 sec)
Time for fast ML tree search: 0.009 seconds
NOTE: ModelFinder requires 0 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 1425) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 4788.371 15 9606.743 9607.083 9685.671
2 GTR+F+I 4701.476 16 9434.951 9435.338 9519.142
3 GTR+F+G4 4700.958 16 9433.916 9434.303 9518.107
4 GTR+F+I+G4 4700.796 17 9435.591 9436.026 9525.044
6 SYM+I 4755.755 13 9537.510 9537.768 9605.915
7 SYM+G4 4756.304 13 9538.609 9538.867 9607.014
8 SYM+I+G4 4756.016 14 9540.031 9540.329 9613.698
10 HKY+F+I 4768.665 12 9561.330 9561.551 9624.474
11 HKY+F+G4 4770.979 12 9565.958 9566.179 9629.101
12 HKY+F+I+G4 4771.601 13 9569.201 9569.459 9637.607
14 K2P+I 4853.060 9 9724.119 9724.247 9771.477
15 K2P+G4 4856.331 9 9730.661 9730.789 9778.019
16 K2P+I+G4 4856.646 10 9733.292 9733.448 9785.912
18 F81+F+I 4780.098 11 9582.196 9582.383 9640.077
19 F81+F+G4 4782.764 11 9587.527 9587.714 9645.408
20 F81+F+I+G4 4783.308 12 9590.615 9590.836 9653.758
22 JC+I 4857.312 8 9730.625 9730.726 9772.720
23 JC+G4 4860.963 8 9737.926 9738.028 9780.021
24 JC+I+G4 4861.282 9 9740.565 9740.692 9787.922
Akaike Information Criterion: GTR+F+G4
Corrected Akaike Information Criterion: GTR+F+G4
Bayesian Information Criterion: GTR+F+G4
Best-fit model: GTR+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000005/OG0000005.cds.model.gz
CPU time for ModelFinder: 0.079 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.084 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 29709)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -4700.958
Optimal log-likelihood: -4700.957
Rate parameters: A-C: 2.05067 A-G: 2.05192 A-T: 4.49880 C-G: 0.90182 C-T: 6.94984 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.163 G: 0.225 T: 0.314
Gamma shape alpha: 0.356
Parameters optimization took 1 rounds (0.001 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000173815 secs using 99.53% CPU
Computing ML distances took 0.000224 sec (of wall-clock time) 0.000227 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.45247e-05 secs using 96.58% CPU
Constructing RapidNJ tree: done in 3.44068e-05 secs using 95.91% CPU
Computing RapidNJ tree took 0.000152 sec (of wall-clock time) 0.000152 sec (of CPU time)
Log-likelihood of RapidNJ tree: -4700.957
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.020 second
Computing log-likelihood of 4 initial trees ... 0.001 seconds
Current best score: -4700.957
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.00103143 secs using 99.67% CPU
Optimizing NNI: done in 0.00202211 secs using 99.9% CPU
Optimizing NNI: done in 0.00207973 secs using 99.87% CPU
Optimizing NNI: done in 0.00205632 secs using 99.89% CPU
Optimizing NNI: done in 0.00204108 secs using 99.9% CPU
Finish initializing candidate tree set (5)
Current best tree score: -4700.957 / CPU time: 0.036
Number of iterations: 5
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.000914596 secs using 99.61% CPU
Optimizing NNI: done in 0.00290653 secs using 99.91% CPU
Optimizing NNI: done in 0.00197357 secs using 99.87% CPU
Optimizing NNI: done in 0.00282874 secs using 99.9% CPU
Optimizing NNI: done in 0.00273096 secs using 99.89% CPU
Iteration 10 / LogL: -4700.961 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00283278 secs using 99.9% CPU
Optimizing NNI: done in 0.000802524 secs using 99.81% CPU
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Optimizing NNI: done in 0.00176974 secs using 99.9% CPU
Optimizing NNI: done in 0.00273525 secs using 99.92% CPU
Iteration 20 / LogL: -4700.960 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00278982 secs using 99.93% CPU
Optimizing NNI: done in 0.00171614 secs using 99.88% CPU
UPDATE BEST LOG-LIKELIHOOD: -4700.957
Optimizing NNI: done in 0.00286669 secs using 99.91% CPU
Optimizing NNI: done in 0.000848763 secs using 99.79% CPU
Optimizing NNI: done in 0.00269795 secs using 99.93% CPU
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Optimizing NNI: done in 0.00289316 secs using 99.93% CPU
Optimizing NNI: done in 0.00301835 secs using 99.92% CPU
Iteration 30 / LogL: -4700.980 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.000817239 secs using 99.6% CPU
Optimizing NNI: done in 0.000854053 secs using 99.64% CPU
Optimizing NNI: done in 0.00192904 secs using 99.84% CPU
Optimizing NNI: done in 0.00277961 secs using 99.8% CPU
Optimizing NNI: done in 0.000854641 secs using 99.81% CPU
Optimizing NNI: done in 0.00286656 secs using 99.91% CPU
Optimizing NNI: done in 0.00180625 secs using 99.88% CPU
UPDATE BEST LOG-LIKELIHOOD: -4700.957
Optimizing NNI: done in 0.00286637 secs using 99.92% CPU
Optimizing NNI: done in 0.00200877 secs using 99.91% CPU
Optimizing NNI: done in 0.0027409 secs using 99.93% CPU
Iteration 40 / LogL: -4701.116 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00263513 secs using 99.92% CPU
Optimizing NNI: done in 0.00285406 secs using 99.93% CPU
Optimizing NNI: done in 0.00178181 secs using 99.9% CPU
Optimizing NNI: done in 0.0017949 secs using 99.89% CPU
Optimizing NNI: done in 0.00279485 secs using 96.21% CPU
Optimizing NNI: done in 0.00183029 secs using 99.88% CPU
Optimizing NNI: done in 0.00283989 secs using 99.69% CPU
Optimizing NNI: done in 0.0018305 secs using 99.86% CPU
Optimizing NNI: done in 0.00197412 secs using 99.89% CPU
Optimizing NNI: done in 0.00254906 secs using 99.68% CPU
Iteration 50 / LogL: -4700.961 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4726.308
Optimizing NNI: done in 0.00182699 secs using 99.84% CPU
Optimizing NNI: done in 0.00180623 secs using 99.88% CPU
Optimizing NNI: done in 0.00175928 secs using 99.87% CPU
Optimizing NNI: done in 0.00263804 secs using 99.92% CPU
Optimizing NNI: done in 0.00175611 secs using 99.88% CPU
Optimizing NNI: done in 0.00269479 secs using 99.93% CPU
Optimizing NNI: done in 0.00175355 secs using 99.85% CPU
Optimizing NNI: done in 0.00266942 secs
Optimizing NNI: done in 0.0025837 secs using 98.7% CPU
Optimizing NNI: done in 0.00270775 secs using 99.94% CPU
Iteration 60 / LogL: -4701.063 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.000798374 secs using 99.83% CPU
Optimizing NNI: done in 0.00187384 secs using 99.63% CPU
Optimizing NNI: done in 0.00183468 secs using 99.91% CPU
Optimizing NNI: done in 0.00169351 secs using 99.91% CPU
Optimizing NNI: done in 0.00078693 secs using 99.75% CPU
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Optimizing NNI: done in 0.00196345 secs using 99.88% CPU
Optimizing NNI: done in 0.000873715 secs using 99.8% CPU
Iteration 70 / LogL: -4707.866 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00182785 secs using 99.84% CPU
Optimizing NNI: done in 0.00283072 secs using 99.94% CPU
Optimizing NNI: done in 0.00292873 secs using 99.94% CPU
Optimizing NNI: done in 0.000830561 secs using 99.81% CPU
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Optimizing NNI: done in 0.00260652 secs using 99.9% CPU
Iteration 80 / LogL: -4700.961 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00186914 secs using 99.3% CPU
Optimizing NNI: done in 0.00292427 secs using 99.92% CPU
Optimizing NNI: done in 0.00176232 secs using 99.87% CPU
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Optimizing NNI: done in 0.00257524 secs using 99.91% CPU
Optimizing NNI: done in 0.00185541 secs using 99.87% CPU
Iteration 90 / LogL: -4701.064 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00078243 secs using 99.82% CPU
Optimizing NNI: done in 0.000866033 secs using 99.77% CPU
Optimizing NNI: done in 0.00179677 secs using 99.9% CPU
Optimizing NNI: done in 0.00175368 secs using 99.9% CPU
Optimizing NNI: done in 0.00285775 secs using 99.94% CPU
Optimizing NNI: done in 0.00273886 secs using 99.9% CPU
Optimizing NNI: done in 0.00282019 secs using 99.92% CPU
Optimizing NNI: done in 0.00276386 secs using 99.93% CPU
Optimizing NNI: done in 0.00285754 secs using 99.95% CPU
Optimizing NNI: done in 0.00275715 secs using 99.96% CPU
Iteration 100 / LogL: -4700.960 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4727.132
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00189707 secs using 99.84% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4700.957
Optimal log-likelihood: -4700.956
Rate parameters: A-C: 2.05033 A-G: 2.05150 A-T: 4.50398 C-G: 0.91194 C-T: 6.95414 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.163 G: 0.225 T: 0.314
Gamma shape alpha: 0.356
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -4700.956
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000005/OG0000005.cds.splits.nex
Total tree length: 0.652
Total number of iterations: 101
CPU time used for tree search: 0.675 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.681 sec (0h:0m:0s)
Total CPU time used: 0.733 sec (0h:0m:0s)
Total wall-clock time used: 0.739 sec (0h:0m:0s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000005/OG0000005.cds.splits.nex...
5 taxa and 13 splits.
Consensus tree written to results/gene_tree/OG0000005/OG0000005.cds.contree
Reading input trees file results/gene_tree/OG0000005/OG0000005.cds.contree
Log-likelihood of consensus tree: -4700.956
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000005/OG0000005.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000005/OG0000005.cds.treefile
Likelihood distances: results/gene_tree/OG0000005/OG0000005.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000005/OG0000005.cds.splits.nex
Consensus tree: results/gene_tree/OG0000005/OG0000005.cds.contree
Screen log file: results/gene_tree/OG0000005/OG0000005.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000005/OG0000005.cds.treefile -m "GTR{2.05033,2.0515,4.50398,0.911943,6.95414}+F{0.298386,0.162667,0.224842,0.314105}+G4{0.355864}" --length 1425
Date and Time: Mon Oct 2 04:11:46 2023
OG0000002
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/alignment/trimmed_cds/OG0000002.trimmed.cds.alignment.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 172830
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 5 sequences with 960 nucleotide sites
Number of constant sites: 490 (= 51.0417% of all sites)
Number of invariant (constant or ambiguous constant) sites: 490 (= 51.0417% of all sites)
Number of parsimony informative sites: 141
Number of distinct site patterns: 253
ModelFinder
-----------
Best-fit model according to BIC: HKY+F+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
HKY+F+G4 -3870.800 7765.600 - 0.000662 7765.929 - 0.000758 7824.003 + 0.702
HKY+F+I -3872.321 7768.641 - 0.000145 7768.971 - 0.000166 7827.044 + 0.153
F81+F+G4 -3876.741 7775.482 - 4.73e-06 7775.761 - 5.55e-06 7829.019 + 0.0572
GTR+F+G4 -3860.043 7752.086 + 0.57 7752.663 + 0.576 7829.957 - 0.0357
HKY+F+I+G4 -3870.644 7767.289 - 0.000285 7767.673 - 0.000317 7830.559 - 0.0265
F81+F+I -3878.146 7778.293 - 1.16e-06 7778.571 - 1.36e-06 7831.829 - 0.014
GTR+F+I -3861.549 7755.098 + 0.126 7755.675 + 0.128 7832.969 - 0.00793
F81+F+I+G4 -3876.653 7777.306 - 1.9e-06 7777.635 - 2.18e-06 7835.709 - 0.00201
GTR+F+I+G4 -3859.674 7753.348 + 0.303 7753.998 + 0.295 7836.086 - 0.00167
GTR+F -3915.041 7860.081 - 2.02e-24 7860.590 - 2.11e-24 7933.085 - 1.44e-24
SYM+G4 -3973.305 7972.610 - 7.4e-49 7972.995 - 8.24e-49 8035.880 - 6.88e-47
SYM+I -3975.670 7977.341 - 6.95e-50 7977.725 - 7.74e-50 8040.611 - 6.46e-48
SYM+I+G4 -3973.765 7975.529 - 1.72e-49 7975.974 - 1.86e-49 8043.666 - 1.4e-48
JC+G4 -4022.390 8060.780 - 5.29e-68 8060.932 - 6.61e-68 8099.716 - 9.46e-61
JC+I -4022.703 8061.406 - 3.87e-68 8061.557 - 4.84e-68 8100.341 - 6.92e-61
JC+I+G4 -4022.103 8062.206 - 2.59e-68 8062.395 - 3.18e-68 8106.008 - 4.07e-62
K2P+G4 -4022.261 8062.521 - 2.22e-68 8062.710 - 2.72e-68 8106.323 - 3.48e-62
K2P+I -4022.620 8063.241 - 1.55e-68 8063.430 - 1.9e-68 8107.043 - 2.43e-62
K2P+I+G4 -4021.992 8063.984 - 1.07e-68 8064.215 - 1.28e-68 8112.653 - 1.47e-63
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: HKY+F+G4
Rate parameter R:
A-C: 1.0000
A-G: 1.4960
A-T: 1.0000
C-G: 1.0000
C-T: 1.4960
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.373
pi(C) = 0.1543
pi(G) = 0.149
pi(T) = 0.3237
Rate matrix Q:
A -0.8602 0.1894 0.2735 0.3973
C 0.4579 -1.235 0.1828 0.5943
G 0.685 0.1894 -1.272 0.3973
T 0.4579 0.2834 0.1828 -0.9241
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.6554
Category Relative_rate Proportion
1 0.0647 0.25
2 0.3417 0.25
3 0.9071 0.25
4 2.686 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -3870.8000 (s.e. 73.2806)
Unconstrained log-likelihood (without tree): -3797.2410
Number of free parameters (#branches + #model parameters): 12
Akaike information criterion (AIC) score: 7765.5999
Corrected Akaike information criterion (AICc) score: 7765.9294
Bayesian information criterion (BIC) score: 7824.0031
Total tree length (sum of branch lengths): 1.1864
Sum of internal branch lengths: 0.1537 (12.9537% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Caulerpa_cliftonii_HV03798' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+----------------------------------Caulerpa_cliftonii_HV03798
|
| +------------------------------------------Avrainvillea_mazei_HV02664
+---------------| (99)
| +-----------------------------------Bryopsis_plumosa_WEST4718
|
| +---------------------Chlorodesmis_fastigiata_HV03865
+----| (82)
+----------Flabellia_petiolata_HV01202
Tree in newick format:
(Caulerpa_cliftonii_HV03798:0.2450039594,(Avrainvillea_mazei_HV02664:0.3017113597,Bryopsis_plumosa_WEST4718:0.2547154404)99:0.1162397061,(Chlorodesmis_fastigiata_HV03865:0.1545269317,Flabellia_petiolata_HV01202:0.0767770898)82:0.0374462697);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -3870.799971
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+----------------------------------Caulerpa_cliftonii_HV03798
|
| +------------------------------------------Avrainvillea_mazei_HV02664
+---------------| (99)
| +-----------------------------------Bryopsis_plumosa_WEST4718
|
| +---------------------Chlorodesmis_fastigiata_HV03865
+----| (82)
+----------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Caulerpa_cliftonii_HV03798:0.2449010150,(Avrainvillea_mazei_HV02664:0.3016949583,Bryopsis_plumosa_WEST4718:0.2547536578)99:0.1161341663,(Chlorodesmis_fastigiata_HV03865:0.1545129855,Flabellia_petiolata_HV01202:0.0767861542)82:0.0374701837);
TIME STAMP
----------
Date and time: Mon Oct 2 04:11:48 2023
Total CPU time used: 0.824548 seconds (0h:0m:0s)
Total wall-clock time used: 0.8536361903 seconds (0h:0m:0s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000002.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000002/OG0000002.cds -redo
Seed: 172830 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:11:47 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000002.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.000127539 secs using 98.01% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000963166 secs using 27.41% CPU
Alignment has 5 sequences with 960 columns, 253 distinct patterns
141 parsimony-informative, 329 singleton sites, 489 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 9.90182e-06 secs
1 Caulerpa_cliftonii_HV03798 2.19% passed 91.35%
2 Avrainvillea_mazei_HV02664 2.50% passed 16.42%
3 Chlorodesmis_fastigiata_HV03865 3.44% passed 89.63%
4 Flabellia_petiolata_HV01202 5.62% passed 96.08%
5 Bryopsis_plumosa_WEST4718 0.94% passed 78.86%
**** TOTAL 2.94% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 2.11075e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.000831895 secs using 83.06% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -3859.724
Optimal log-likelihood: -3859.712
Rate parameters: A-C: 3.23564 A-G: 3.86765 A-T: 3.19632 C-G: 3.99265 C-T: 4.79502 G-T: 1.00000
Base frequencies: A: 0.373 C: 0.154 G: 0.149 T: 0.324
Proportion of invariable sites: 0.256
Gamma shape alpha: 1.635
Parameters optimization took 1 rounds (0.002 sec)
Time for fast ML tree search: 0.010 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 960) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 3915.041 15 7860.081 7860.590 7933.085
2 GTR+F+I 3861.549 16 7755.098 7755.675 7832.969
3 GTR+F+G4 3860.043 16 7752.086 7752.663 7829.957
4 GTR+F+I+G4 3859.674 17 7753.348 7753.998 7836.086
6 SYM+I 3975.670 13 7977.341 7977.725 8040.611
7 SYM+G4 3973.305 13 7972.610 7972.995 8035.880
8 SYM+I+G4 3973.765 14 7975.529 7975.974 8043.666
10 HKY+F+I 3872.321 12 7768.641 7768.971 7827.044
11 HKY+F+G4 3870.800 12 7765.600 7765.929 7824.003
12 HKY+F+I+G4 3870.644 13 7767.289 7767.673 7830.559
14 K2P+I 4022.620 9 8063.241 8063.430 8107.043
15 K2P+G4 4022.261 9 8062.521 8062.710 8106.323
16 K2P+I+G4 4021.992 10 8063.984 8064.215 8112.653
18 F81+F+I 3878.146 11 7778.293 7778.571 7831.829
19 F81+F+G4 3876.741 11 7775.482 7775.761 7829.019
20 F81+F+I+G4 3876.653 12 7777.306 7777.635 7835.709
22 JC+I 4022.703 8 8061.406 8061.557 8100.341
23 JC+G4 4022.390 8 8060.780 8060.932 8099.716
24 JC+I+G4 4022.103 9 8062.206 8062.395 8106.008
Akaike Information Criterion: GTR+F+G4
Corrected Akaike Information Criterion: GTR+F+G4
Bayesian Information Criterion: HKY+F+G4
Best-fit model: HKY+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000002/OG0000002.cds.model.gz
CPU time for ModelFinder: 0.094 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.097 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 172830)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -3870.800
Optimal log-likelihood: -3870.800
Rate parameters: A-C: 1.00000 A-G: 1.49602 A-T: 1.00000 C-G: 1.00000 C-T: 1.49602 G-T: 1.00000
Base frequencies: A: 0.373 C: 0.154 G: 0.149 T: 0.324
Gamma shape alpha: 0.655
Parameters optimization took 1 rounds (0.001 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000157058 secs using 96.78% CPU
Computing ML distances took 0.000205 sec (of wall-clock time) 0.000203 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.49209e-05 secs using 94.5% CPU
Constructing RapidNJ tree: done in 3.65525e-05 secs using 95.75% CPU
Computing RapidNJ tree took 0.000147 sec (of wall-clock time) 0.000142 sec (of CPU time)
Log-likelihood of RapidNJ tree: -3870.800
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.021 second
Computing log-likelihood of 4 initial trees ... 0.001 seconds
Current best score: -3870.800
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.00129186 secs using 99.86% CPU
Optimizing NNI: done in 0.00243441 secs using 99.94% CPU
Optimizing NNI: done in 0.00246266 secs using 99.89% CPU
Optimizing NNI: done in 0.00250812 secs using 99.92% CPU
Optimizing NNI: done in 0.00265981 secs using 99.89% CPU
Finish initializing candidate tree set (5)
Current best tree score: -3870.800 / CPU time: 0.039
Number of iterations: 5
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00238388 secs using 99.92% CPU
Optimizing NNI: done in 0.00352721 secs using 99.94% CPU
Optimizing NNI: done in 0.00239861 secs using 99.93% CPU
Optimizing NNI: done in 0.00214361 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -3870.800
Optimizing NNI: done in 0.00353469 secs using 99.92% CPU
Iteration 10 / LogL: -3871.141 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00342582 secs using 99.95% CPU
Optimizing NNI: done in 0.00346122 secs using 99.96% CPU
Optimizing NNI: done in 0.00346096 secs using 99.94% CPU
Optimizing NNI: done in 0.00349569 secs using 99.95% CPU
Optimizing NNI: done in 0.00215391 secs using 99.91% CPU
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Optimizing NNI: done in 0.00354677 secs using 99.92% CPU
Optimizing NNI: done in 0.00249636 secs using 99.91% CPU
Optimizing NNI: done in 0.00242063 secs
Iteration 20 / LogL: -3871.038 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00379407 secs
Optimizing NNI: done in 0.00382596 secs using 99.95% CPU
Optimizing NNI: done in 0.00102624 secs using 95.88% CPU
Optimizing NNI: done in 0.00347608 secs using 99.94% CPU
Optimizing NNI: done in 0.00225665 secs using 99.93% CPU
Optimizing NNI: done in 0.00402471 secs using 99.91% CPU
Optimizing NNI: done in 0.00359762 secs using 99.93% CPU
Optimizing NNI: done in 0.00241645 secs using 99.86% CPU
Optimizing NNI: done in 0.0037039 secs using 99.89% CPU
Optimizing NNI: done in 0.00357915 secs using 99.91% CPU
Iteration 30 / LogL: -3870.861 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00358842 secs using 99.9% CPU
Optimizing NNI: done in 0.00356638 secs using 99.91% CPU
Optimizing NNI: done in 0.00256011 secs using 99.88% CPU
Optimizing NNI: done in 0.00223748 secs using 95.78% CPU
Optimizing NNI: done in 0.00248451 secs using 99.9% CPU
Optimizing NNI: done in 0.00353735 secs
Optimizing NNI: done in 0.00379583 secs using 98.16% CPU
Optimizing NNI: done in 0.00357983 secs using 99.89% CPU
Optimizing NNI: done in 0.00379177 secs using 99.9% CPU
Optimizing NNI: done in 0.00356102 secs using 99.92% CPU
Iteration 40 / LogL: -3870.970 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00364818 secs using 99.91% CPU
Optimizing NNI: done in 0.00387165 secs using 99.93% CPU
Optimizing NNI: done in 0.00224711 secs using 99.77% CPU
Optimizing NNI: done in 0.0025024 secs using 99.9% CPU
Optimizing NNI: done in 0.00361217 secs using 99.86% CPU
Optimizing NNI: done in 0.00242084 secs using 99.88% CPU
Optimizing NNI: done in 0.00357728 secs
Optimizing NNI: done in 0.00355388 secs using 98.37% CPU
Optimizing NNI: done in 0.00243712 secs using 99.87% CPU
Optimizing NNI: done in 0.00230107 secs using 99.87% CPU
Iteration 50 / LogL: -3870.832 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -3885.586
Optimizing NNI: done in 0.00264465 secs using 99.86% CPU
Optimizing NNI: done in 0.00367332 secs using 99.91% CPU
Optimizing NNI: done in 0.00357313 secs using 99.91% CPU
Optimizing NNI: done in 0.00236703 secs using 99.87% CPU
Optimizing NNI: done in 0.0024179 secs using 99.84% CPU
Optimizing NNI: done in 0.00230084 secs using 99.88% CPU
Optimizing NNI: done in 0.0035639 secs using 99.92% CPU
Optimizing NNI: done in 0.00229128 secs using 99.81% CPU
Optimizing NNI: done in 0.00357507 secs using 99.91% CPU
Optimizing NNI: done in 0.00359932 secs using 99.91% CPU
Iteration 60 / LogL: -3870.808 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00358825 secs using 99.94% CPU
Optimizing NNI: done in 0.00241978 secs using 99.88% CPU
Optimizing NNI: done in 0.00363041 secs using 99.93% CPU
Optimizing NNI: done in 0.00369456 secs using 99.93% CPU
Optimizing NNI: done in 0.00221287 secs using 99.87% CPU
Optimizing NNI: done in 0.00242964 secs using 99.89% CPU
Optimizing NNI: done in 0.00226534 secs using 99.9% CPU
Optimizing NNI: done in 0.00358936 secs using 99.91% CPU
Optimizing NNI: done in 0.00258309 secs using 99.84% CPU
Optimizing NNI: done in 0.00243052 secs using 99.81% CPU
Iteration 70 / LogL: -3870.854 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00265668 secs using 99.86% CPU
Optimizing NNI: done in 0.00349647 secs using 99.9% CPU
Optimizing NNI: done in 0.00343105 secs using 99.91% CPU
Optimizing NNI: done in 0.00342038 secs using 99.9% CPU
Optimizing NNI: done in 0.00115584 secs using 99.75% CPU
Optimizing NNI: done in 0.00225989 secs using 99.87% CPU
Optimizing NNI: done in 0.00352134 secs using 99.91% CPU
Optimizing NNI: done in 0.0035463 secs using 99.88% CPU
Optimizing NNI: done in 0.00340671 secs using 99.89% CPU
Optimizing NNI: done in 0.00236575 secs using 99.84% CPU
Iteration 80 / LogL: -3870.821 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00361472 secs using 99.9% CPU
Optimizing NNI: done in 0.00357711 secs using 99.89% CPU
Optimizing NNI: done in 0.00109541 secs using 99.78% CPU
Optimizing NNI: done in 0.00115481 secs using 99.76% CPU
Optimizing NNI: done in 0.00253766 secs
Optimizing NNI: done in 0.00230191 secs using 99.87% CPU
Optimizing NNI: done in 0.00240336 secs using 99.49% CPU
Optimizing NNI: done in 0.00107651 secs using 99.77% CPU
Optimizing NNI: done in 0.00242538 secs using 99.86% CPU
Optimizing NNI: done in 0.00245991 secs using 99.43% CPU
Iteration 90 / LogL: -3870.854 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00109883 secs using 99.65% CPU
Optimizing NNI: done in 0.00381286 secs using 99.92% CPU
Optimizing NNI: done in 0.00349803 secs using 99.94% CPU
Optimizing NNI: done in 0.00356565 secs using 99.93% CPU
Optimizing NNI: done in 0.00244565 secs using 99.85% CPU
Optimizing NNI: done in 0.00362925 secs using 99.94% CPU
Optimizing NNI: done in 0.00386556 secs using 99.93% CPU
Optimizing NNI: done in 0.00242573 secs using 99.85% CPU
Optimizing NNI: done in 0.0026259 secs using 99.85% CPU
Optimizing NNI: done in 0.00368061 secs using 99.9% CPU
Iteration 100 / LogL: -3870.946 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -3885.737
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00390401 secs using 99.9% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -3870.800
Optimal log-likelihood: -3870.800
Rate parameters: A-C: 1.00000 A-G: 1.49602 A-T: 1.00000 C-G: 1.00000 C-T: 1.49602 G-T: 1.00000
Base frequencies: A: 0.373 C: 0.154 G: 0.149 T: 0.324
Gamma shape alpha: 0.655
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -3870.800
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000002/OG0000002.cds.splits.nex
Total tree length: 1.186
Total number of iterations: 101
CPU time used for tree search: 0.777 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.799 sec (0h:0m:0s)
Total CPU time used: 0.825 sec (0h:0m:0s)
Total wall-clock time used: 0.846 sec (0h:0m:0s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000002/OG0000002.cds.splits.nex...
5 taxa and 11 splits.
Consensus tree written to results/gene_tree/OG0000002/OG0000002.cds.contree
Reading input trees file results/gene_tree/OG0000002/OG0000002.cds.contree
Log-likelihood of consensus tree: -3870.800
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000002/OG0000002.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000002/OG0000002.cds.treefile
Likelihood distances: results/gene_tree/OG0000002/OG0000002.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000002/OG0000002.cds.splits.nex
Consensus tree: results/gene_tree/OG0000002/OG0000002.cds.contree
Screen log file: results/gene_tree/OG0000002/OG0000002.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000002/OG0000002.cds.treefile -m "HKY{1.49602}+F{0.373041,0.154325,0.148959,0.323675}+G4{0.655388}" --length 960
Date and Time: Mon Oct 2 04:11:48 2023
Supertree
Workflow
Bibliography
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@article{10.1093/molbev/mst010,
author = "Katoh, Kazutaka and Standley, Daron M.",
title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
journal = "Molecular Biology and Evolution",
volume = "30",
number = "4",
pages = "772-780",
year = "2013",
month = "01",
abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
issn = "0737-4038",
doi = "10.1093/molbev/mst010",
url = "https://doi.org/10.1093/molbev/mst010",
eprint = "https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf"
}
@article{Emms2019,
author = "Emms, David M. and Kelly, Steven",
type = "Journal Article",
title = "OrthoFinder: phylogenetic orthology inference for comparative genomics",
journal = "Genome Biology",
number = "1",
doi = "10.1186/s13059-019-1832-y",
volume = "20",
pages = "238",
url = "https://doi.org/10.1186/s13059-019-1832-y",
year = "2019",
abstract = "Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.",
isbn = "1474-760X",
DA = "2019/11/14"
}
@article{10.1371/journal.pbio.3001007,
author = "Steenwyk, Jacob L. and Buida, III, Thomas J. and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
doi = "10.1371/journal.pbio.3001007",
journal = "PLOS Biology",
publisher = "Public Library of Science",
title = "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference",
year = "2020",
month = "12",
volume = "18",
url = "https://doi.org/10.1371/journal.pbio.3001007",
pages = "1-17",
abstract = "Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.",
number = "12"
}
@article{Steenwyk_2021,
author = "Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis",
doi = "10.1101/2021.10.02.462868",
url = "https://doi.org/10.1101\%2F2021.10.02.462868",
year = "2021",
month = "oct",
journal = "biorxiv",
publisher = "Cold Spring Harbor Laboratory",
title = "{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data"
}
@article{10.1093/molbev/msx281,
author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
journal = "Molecular Biology and Evolution",
volume = "35",
number = "2",
pages = "518-522",
year = "2017",
month = "10",
abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
issn = "0737-4038",
doi = "10.1093/molbev/msx281",
url = "https://doi.org/10.1093/molbev/msx281",
eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}
@article{10.1093/bioinformatics/btab096,
author = "Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
journal = "Bioinformatics",
volume = "37",
number = "16",
pages = "2325-2331",
year = "2021",
month = "02",
abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
issn = "1367-4803",
doi = "10.1093/bioinformatics/btab096",
url = "https://doi.org/10.1093/bioinformatics/btab096",
eprint = "https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf"
}
@article{eaton_toytree_2020,
author = "Eaton, Deren A. R.",
title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
volume = "11",
doi = "10.1111/2041-210X.13313",
journal = "Methods in Ecology and Evolution",
year = "2020",
pages = "187--191"
}
@article{10.1093/molbev/msaa015,
author = "Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert",
title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
journal = "Molecular Biology and Evolution",
volume = "37",
number = "5",
pages = "1530-1534",
year = "2020",
month = "02",
abstract = "{IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.}",
issn = "0737-4038",
doi = "10.1093/molbev/msaa015",
url = "https://doi.org/10.1093/molbev/msaa015",
eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}
@article{Kalyaanamoorthy2017,
author = "Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas K F and von Haeseler, Arndt and Jermiin, Lars S",
type = "Journal Article",
title = "ModelFinder: fast model selection for accurate phylogenetic estimates",
journal = "Nature Methods",
number = "6",
doi = "10.1038/nmeth.4285",
volume = "14",
pages = "587--589",
url = "https://doi.org/10.1038/nmeth.4285",
year = "2017",
abstract = "ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.",
issn = "1548-7105",
DA = "2017/06/01"
}
@article{Zhang2018,
author = "Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash",
type = "Journal Article",
title = "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees",
journal = "BMC Bioinformatics",
number = "6",
doi = "10.1186/s12859-018-2129-y",
volume = "19",
pages = "153",
url = "https://doi.org/10.1186/s12859-018-2129-y",
year = "2018",
abstract = "Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.",
issn = "1471-2105",
DA = "2018/05/08"
}File(s) not Fasta or Genbank file. Suffix from file 'NC_026795-truncated.txt' is not Fasta or Genbank. File is assumed to be in Fasta format.